bug when running test data

[mol529]

hello！
I ran the LSA with the test data, and had some problem. I don't know how to solve.
The first and second steps succeed, but the third step "bash ReadPartitioning.sh 4" with the problem:

Fri Oct 30 01:57:27 CST 2015 partitioning reads in hashed input file 4
printing end of last log file...
Traceback (most recent call last):
File "LSA/write_partition_parts.py", line 71, in
G = [open('%s%s.%s.cols.%d' % (tmpdir,sample_id,outpart,i),'w') for i in range(0,2hashobject.hash_size,2hashobject.hash_size/5
0)]
ValueError: range() step argument must not be zeroG = [open('%s%s.%s.cols.%d' % (tmpdir,sample_id,outpart,i),'w') for i in range(0
,2hashobject.hash_size,2hashobject.hash_size/50)]

G = [open('%s%s.%s.cols.%d' % (tmpdir,sample_id,outpart,i),'w') for i in range(0,2**hashobject.hash_size,2**hashobject.hash_size/5

0)]
ValueErrorValueError: : range() step argument must not be zerorange() step argument must not be zeroG = [open('%s%s.%s.cols.%d' %
(tmpdir,sample_id,outpart,i),'w') for i in range(0,2hashobject.hash_size,2hashobject.hash_size/50)]

And my datasets are more than 30Gb. Can I run it with qsub instead of bsub?

Thanks!

[nmb85]

"Can I run it with qsub instead of bsub?"
FWIW, I've been running my jobs with qsub without any problems. This PDF gives you a one-for-one conversion between the qsub (SGE) and bsub (LSF) options. Maybe later this weekend I'll post a modified create_jobs.py for SGE.

Here is an example of an LSF script modified for SGE. the header, PATH, and SGE_TASK_ID need to be changed:

#!/bin/bash
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -N KmerCorpus
#$ -t 1-6:1
#$ -o ./Logs/KmerCorpus.out
#$ -e ./Logs/KmerCorpus.err
#$ -q micro
PATH=...
export PATH
echo Date: `date`
t1=`date +%s`
sleep $(($SGE_TASK_ID % 60))
python LSA/kmer_corpus.py -r ${SGE_TASK_ID} -i ./hashed_reads/ -o ./cluster_vectors/
[ $? -eq 0 ] || echo 'JOB FAILURE: $?'
echo Date: `date`
t2=`date +%s`
tdiff=`echo 'scale=3;('$t2'-'$t1')/3600' | bc`
echo 'Total time:  '$tdiff' hours'

[brian-cleary]

Sorry for the slow response.

That's great about converting over to qsub! So we're you able to get past
your original error?

On Mon, Nov 2, 2015 at 10:39 PM, russianconcussion <[email protected]

wrote:

Can I run it with qsub instead of bsub?
FWIW, I've been running my jobs with qsub without any problems. This PDF
http://www.med.upenn.edu/hpc/assets/user-content/documents/SGE_to_LSF_User_Migration_Guide.pdf
gives you a one-for-one conversion between the qsub (SGE) and bsub (LSF)
options.

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